Hi All-
New modules are available in the core and in bioperl-run for
working with Heng Li's short read assembler "maq"
(http://maq.sourceforge.net/maq-man.shtml). Bio::Tools::Run::Maq
allows a quick assembly call with a canned a maq pipeline, and also
allows individual maq commands to be called separately.
It uses Bio::Assembly::IO::maq (a read-only module) to deliver
a Bio::Assembly::Scaffold from maq output.
If you're interested, see
http://www.bioperl.org/wiki/HOWTO:Short-read_assemblies_with_maq
and update your core and bioperl-run. The code inherits from Florent's
excellent new Bio::Tools::Run::AssemblerBase -- kudos to him!!
tests are in bioperl-run/trunk/t/Maq.t, see them for myriad examples
send me the bugs
MAJ